After standard seawalls have been built successfully, fishery ports become the structures most easily damaged during a typhoon. Estimating the risk of fishery ports against typhoons would be useful for identifying weaknesses and implementing corrective measures to protect fishing boats from a typhoon. This study describes a versatile methodology for conducting this type of quantitative assessment at fishery ports. The Dongsha fishery port in Zhejiang Province was selected as a case study to test the results derived from a high-precision Hydrodynamic Flexible Mesh model coupled with the Spectral Wave model. First, typhoon characteristics were assessed based on historical typhoons in the study area, and then, the wind, tide, storm surge, and waves were modeled and tide-surge interactions were investigated. Through comparisons of the destructive parameters from the typhoon assessment with the design and structural parameters of the fishery port, the level of the Dongsha fishery port against typhoons was determined to be 12, and the main weaknesses of the port’s defenses were found to be located near feature points T2, T3, T8, and T15. The results obtained demonstrate that the proposed methodology can be used to acquire valuable information on the risk of fishery ports against typhoons.